Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow.

Anna Lopatina,Vjacheslav Krylenkov,Maria D Logacheva,Sofia Medvedeva,Konstantin Severinov,Sergey Shmakov

doi:10.3389/fmicb.2016.00398

Abstract

The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.

Highlights

Snow covers about 35% of the Earth’s surface—permanently or for varying times during the year— and is a major climatic and ecological system (Miteva, 2008)
We studied the bacterial diversity of surface snow from two Russian Antarctic stations, Leningradskaja and Druzhnaja, by analyzing individual 16S rRNA gene fragments cloned after PCR amplification of DNA from melted snow samples collected during the 54th (2009) and 55th (2010) Russian Antarctic expeditions (Lopatina et al, 2013)
To access bacterial diversity in snow samples, a fragment of bacterial 16S rRNA gene was amplified from total DNA following by Illumina pair-end high throughput sequencing (HTS)

Summary

Introduction

Snow covers about 35% of the Earth’s surface—permanently or for varying times during the year— and is a major climatic and ecological system (Miteva, 2008) It directly affects climate, moisture budget and sea level, and serves as an interface between different ecosystems (Pomeroy and Brun, 2001; Davis et al, 2005; Zhang, 2005; Hinkler et al, 2008). Bacterial Diversity of Antarctic Snow on South Pole (Carpenter et al, 2000) to 102–105 in high mountain and Arctic snow (Segawa et al, 2005; Amato et al, 2007; Liu et al, 2009; Harding et al, 2011). A metagenomic study of Arctic spring snow suggested that snow bacteria can be adapted to photochemical reactions and oxidative stress in addition to cold stress (Maccario et al, 2014), and may form specific communities

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Results

Conclusion